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You should be able to get your bookmarks back from your Time machine backup. You can either do this from within Finder or from Time Machine.

Go to your user folder then follow this path Library/Caches/Metadata/Safari Inside that Safari folder are two others Bookmarks and History. Copy the appropriate folder to the same location on your boot drive.

If you are not using Snow Leopard (10.6) let us know. Other versions of the OS store the files in slightly different locations I think.

"Got Time to breathe. You got time for music." Denver Pyle as Briscoe Darling